I'd Like to think I am pretty familiar with pokemon, at least the first few generations. I think black/white was the last game I played. Watched a bit of the show back in the late 90's.
I don't even go that far out. Basically got to the second generation with Silver/Gold and stopped there, but I was a big fan up through then and I watched the anime up to a point.
Assuming this is a pretty straightforward game, team rocket (Jesse and James) or Giovonni are probably scum. Given this is Poly's first game I am not expecting some crazy thematic twist.
I'd say that's most likely. I've thought through a few other plausible, though less obvious, scenarios. We could be dealing with a main cast vs. rivals situation (there are at least a couple of main rivals, including Gary Oak, who you've already pointed out), trainers vs. parents/professors (a bit more of a stretch, but this would be with Prof. Oak and Ash's mother as scum), or main cast vs. active gym leaders (Misty and Brock would be town, Lt. Surge and Blaine would be scum). Everyone vs. the Team Rocket organization still makes the most sense, but I'd consider these as well.
